gitlab.cirad.fr / agap 20 Repositories
Dépôt de code de l'UMR AGAP. Référents : [Alice BOIZET](mailto:alice.boizet@cirad.fr), [Julien FROUIN](mailto:julien.frouin@cirad.fr), [Simon RIO](mailto:simon.rio@cirad.fr), [Stephanie SIDIBE-BOCS](mailto:stephanie.sidibe-bocs@cirad@cirad.fr)
agap/workflows/rna_seq
A Snakemake workflow for producing count matrix suitable for differential expression analysis and formatted for DIANE.
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agap/bioinformatics/training_teaching/muse_lmd5_bioagro_ue_haa906v_bogc/2022_student
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agap/workflows/GATK
A snakemake workflow for SNP Calling using GATK4
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agap/workflows/comparativegenomics
A Snakemake workflow to identify syntenic blocks and orthogroup for a set of species
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agap/workflows/funcannotate
# A snakemake workflow for functional annotation
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agap/bioinformatics/training_teaching/operating_method
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agap/workflows/genomeassembly
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agap/workflows/gene-family
A snakemake workflow for phylogenetic analysis of protein families
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agap/workflows/cutandtag
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agap/workflows/snakeblast
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agap/workflows/indexing_genome
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agap/giv/sorghum_bcnam_analysis
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agap/workflows/cactus-pangenome
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agap/bioinformatics/training_teaching/muse_lmd5_bioagro_ue_haa906v_bogc/2021_student
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agap/bioinformatics/training_teaching/genomehubuse/vgh
Examples of how to use the Vanilla Genome Hub
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agap/bioinformatics/training_teaching/elixir_excelerate_pgaa_2018
Elixir french node (IFB) training on [Plant Genome Assembly and Annotation](https://ressources.france-bioinformatique.fr/fr/evenements/plant-genome-assembly-and-annotation). [ELIXIR-EXCELERATE](https://elixir-europe.org/about-us/how-funded/eu-projects/excelerate) project was funded by the European Commission within the Research Infrastructures programme of Horizon 2020 (grant agreement number 676559).
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